A system that provides a base stabilization system for controlling motion of a controlled structure. The system includes a ground structure such as the floor of a fabrication facility and the controlled structure includes a base on which equipment is mounted. The system also includes at least three air mounts and a plurality of actuators all attached to the ground structure and to the base to isolate the base from the ground structure and to stabilize the base. The system includes a plurality of position and acceleration sensors each of which are co-located with a corresponding actuator. The system also includes a multi-input, multi output feedback control system comprising a computer processor programmed with a feedback control algorithm for controlling each of the actuators based on feedback signals from each of the sensors. The co-location of the sensors with the actuators avoids serious problems resulting from higher order vibration modes.